NDLI: Data Mining and Predictive Modeling of Biomolecular Network from Biomedical Literature Databases

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Issue 1, January 2007

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 3

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 2

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 1

Data Mining and Predictive Modeling of Biomolecular Network from Biomedical Literature Databases

Content Provider	ACM Digital Library
Author	Hu, Xiaohua Wu, Daniel D.
Abstract	In this paper, we present a novel approach Bio-IEDM (Biomedical Information Extraction and Data Mining) to integrate text mining and predictive modeling to analyze biomolecular network from biomedical literature databases. Our method consists of two phases. In phase 1, we discuss a semisupervised efficient learning approach to automatically extract biological relationships such as protein-protein interaction, protein-gene interaction from the biomedical literature databases to construct the biomolecular network. Our method automatically learns the patterns based on a few user seed tuples and then extracts new tuples from the biomedical literature based on the discovered patterns. The derived biomolecular network forms a large scale-free network graph. In phase 2, we present a novel clustering algorithm to analyze the biomolecular network graph to identify biologically meaningful subnetworks (communities). The clustering algorithm considers the characteristics of the scale-free network graphs and is based on the local density of the vertex and its neighborhood functions that can be used to find more meaningful clusters with different density level. The experimental results indicate our approach is very effective in extracting biological knowledge from a huge collection of biomedical literature. The integration of data mining and information extraction provides a promising direction for analyzing the biomolecular network.
Starting Page	251
Ending Page	263
Page Count	13
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2007.070211
Volume Number	4
Issue Number	2
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2007-04-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biomolecular network, semisupervised learning, scale-free network, information extraction, biological complexes (communities).
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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